Remove exit statements by FriederikeHanssen · Pull Request #982 · nf-core/sarek

FriederikeHanssen · 2023-03-29T09:49:39Z

Close #805

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

github-actions · 2023-03-29T10:27:13Z

`nf-core lint` overall result: Passed ✅

Posted for pipeline commit 4b6689b

+| ✅ 151 tests passed       |+
#| ❔   9 tests were ignored |#

Details

❔ Tests ignored:

files_exist - File is ignored: conf/modules.config
files_exist - File is ignored: conf/test.config
files_exist - File is ignored: conf/test_full.config
files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreSchema.groovy
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
template_strings - template_strings

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-sarek_logo_light.png
files_exist - File found: docs/images/nf-core-sarek_logo_light.png
files_exist - File found: docs/images/nf-core-sarek_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreSchema.groovy
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowSarek.groovy
files_exist - File found: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: docs/images/nf-core-sarek_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: '3.2dev'
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 22.10.1, Config: 22.10.1
readme - README Nextflow minimum version in Quick Start section matched config. README: 22.10.1, Config: 22.10.1
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: pytest-workflow.yml
actions_schema_validation - Workflow validation passed: awsfulltest_germline.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.7.2
Run at 2023-03-31 10:26:05

lib/WorkflowMain.groovy

maxulysse · 2023-03-30T12:53:40Z

Asking a second review by @robsyme for sanity

FriederikeHanssen · 2023-03-30T19:54:00Z

I think it is ready, but conda 😡 :

CondaError: No package 'conda-forge/linux-64::libgomp-12.2.0-h65d4601_19' found in cache directories.

where does this come from now. Ahhhhhhhhhrgh

maxulysse · 2023-03-30T20:27:01Z

That's conda, don't wish to much

FriederikeHanssen · 2023-03-31T07:37:42Z

got one conda test to pass by changing nothing, maybe it depends to which runner it is submitted too?

maxulysse · 2023-03-31T08:45:50Z

workflows/sarek.nf

 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */

+import nextflow.Nextflow


I don't think we need that

it failed with missing nextflow.Nextflow before

this commit: https://github.com/nf-core/sarek/actions/runs/4565424537/jobs/8062646459

I think this tests is expected to fail

The import and qualification with nextflow.error prefix are only necessary in Groovy classes pulled into the classpath via inclusion in the lib directory. Inside nextflow files such as main.nf, or workflows/sarek.nf, the error and exit methods are always in scope, so we can remove the import statement and change all occurrences of Nextflow.error to error.

I've just made a bunch of edits. I tried to batch them up, but I am bad at computers and may have messed it up by including some of them as individual commits. It would be good to squash them before any merge or rebase to dev. Apologies for any extra email/notification noise I may have created in the process :(

🤯 I see, thank you for fixing it up ❤️

maxulysse

I don't think we need to have that part in a Nextflow script:

import nextflow.Nextflow

maxulysse · 2023-03-31T08:49:14Z

Amazing work!!!
Thanks

workflows/sarek.nf

We don't need to `import nextflow.Nextflow` inside Nextflow scripts because the methods are already in scope

FriederikeHanssen · 2023-04-17T12:21:00Z

Hey @robsyme ! I just discussed with @subwaystation on how to apply this to other pipelines, and we noticed that there is yet another System.exit call in the initialise function. can it be replaced the same way as all the others, since this time the exitcode is 0:

sarek/lib/WorkflowMain.groovy

Line 53 in 9f3ff50

System.exit(0)

subwaystation · 2023-04-17T13:07:24Z

Hey @robsyme ! I just discussed with @subwaystation on how to apply this to other pipelines, and we noticed that there is yet another System.exit call in the initialise function. can it be replaced the same way as all the others, since this time the exitcode is 0:

sarek/lib/WorkflowMain.groovy

Line 53 in 9f3ff50

System.exit(0)

Also note that in

sarek/lib/WorkflowMain.groovy

Line 64 in 9f3ff50

log.info paramsSummaryLog(workflow, params, log)

there is only a log.info without an actual exit. Just so we don't miss a case.

FriederikeHanssen · 2023-04-19T14:03:12Z

well it appears we have discussed this on slack and my squirrel brain just forgot. For posterity: https://nfcore.slack.com/archives/C04UK9FMKN0/p1680084277233609?thread_ts=1680080487.840229&cid=C04UK9FMKN0

TL;DR: can leave as is or replace with Nextflow.exit(0)

Remove exit statements

150d983

FriederikeHanssen requested a review from maxulysse as a code owner March 29, 2023 09:49

FriederikeHanssen added 2 commits March 29, 2023 14:18

Update changelog

d4d5774

don't lint since we are ahead of template

d3cb234

maxulysse reviewed Mar 30, 2023

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lib/WorkflowMain.groovy Outdated Show resolved Hide resolved

FriederikeHanssen linked an issue Mar 30, 2023 that may be closed by this pull request

Avoid use of exit-statements #805

Closed

FriederikeHanssen marked this pull request as draft March 30, 2023 12:58

FriederikeHanssen added 2 commits March 30, 2023 16:14

address reviews, remove nextflow.warn, replace with log

4b9138c

import nextflow

7c76ff3

FriederikeHanssen marked this pull request as ready for review March 30, 2023 19:54

FriederikeHanssen requested review from maxulysse and robsyme March 30, 2023 20:21

maxulysse reviewed Mar 31, 2023

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maxulysse approved these changes Mar 31, 2023

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robsyme reviewed Mar 31, 2023

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